Cr(VI) contamination is a significant environmental issue, whereas existing remediation technologies, whether physical, chemical, or biological, have many limitations, such as extensive engineering work, high energy consumption, secondary pollution, and incomplete treatment. Here, we report a Cr(VI) remediation method that integrates a natural magnetite/pyrrhotite composite (NMPC) with electrokinetic processes to enhance the remediation efficiency and stability, in which the electron-donating ability of NMPC was utilized to boost the reduction and immobilization of Cr(VI). The XRD analysis shows that NMPC is composed of magnetite and pyrrhotite. A highest 100% Cr(VI) removal efficiency and a TCr removal efficiency over 95% are achieved when treating Cr(VI) contaminants. The remediation stability analysis shows that the redissolution ratio of Cr(VI) in the NMPC-enhanced treatment decreased by more than 62%, indicating that the Cr-containing products were stable and resistant to releasing Cr. Furthermore, the Cr-containing products are analyzed by SEM-EDS, Raman, XRD, and XPS. The results show that the distribution of Cr and Fe is highly correlated and Cr is immobilized in the mineral phase. These results demonstrate that NMPC enhances the removal of Cr(VI) and promotes the immobilization of Cr, thus reducing the risk of Cr reoxidation and contributing to a more durable remediation effect.